For example, if I am Station 1 and my antenna is 20' in the air, my line of sight is 6 miles and Station 2's antenna is 50' in the air, their line of sight is 10 miles. Together, our total line of sight is 16 miles.
Lets assume Station 1's elevation is 300 ft and Station 2 is at sea level. Though Station 2's antenna is higher off the ground, Station 1 is significantly higher. If I account for the elevation change, Station 1's line of sight (at 320 feet) is 25 miles and Station 2's line of sight (at 20 feet) is still 10 miles; making it a total line of sight of 35 miles.
A good example is the space station; they may be using a simple HT with an "antenna height" of 3 feet from the floor; however, since the space station is 254 miles (or 1,341,120 feet) from Earth, their line of sight is 1,414 miles. Which is why someone on Earth with an HT can contact the space station or an orbiting satellite.
So, when accounting for line of sight between two stations, do you account for the elevation difference between the two?